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Holmium in PDB 2bpu: The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction

Enzymatic activity of The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction

All present enzymatic activity of The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction:
3.2.1.17;

Protein crystallography data

The structure of The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction, PDB code: 2bpu was solved by J.Jakoncic, M.Di Michiel, Z.Zhong, V.Honkimaki, Y.Jouanneau, V.Stojanoff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.83 / 1.35
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.707, 78.707, 37.325, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 20.7

Other elements in 2bpu:

The structure of The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Holmium Binding Sites:

The binding sites of Holmium atom in the The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction (pdb code 2bpu). This binding sites where shown within 5.0 Angstroms radius around Holmium atom.
In total 3 binding sites of Holmium where determined in the The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction, PDB code: 2bpu:
Jump to Holmium binding site number: 1; 2; 3;

Holmium binding site 1 out of 3 in 2bpu

Go back to Holmium Binding Sites List in 2bpu
Holmium binding site 1 out of 3 in the The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 1 of The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ho1134

b:29.1
occ:0.50
 O A:HOH2101 2.1 35.3 1.0
OXT A:LEU129 2.4 23.6 1.0
O A:LEU129 2.4 24.2 1.0
C A:LEU129 2.9 24.5 1.0
CA A:LEU129 4.4 24.6 1.0
NZ A:LYS13 4.6 24.0 1.0
CE A:LYS13 4.9 22.5 1.0

Holmium binding site 2 out of 3 in 2bpu

Go back to Holmium Binding Sites List in 2bpu
Holmium binding site 2 out of 3 in the The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 2 of The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ho1135

b:27.4
occ:1.00
 OD2 A:ASP101 2.3 20.3 1.0
O A:HOH2104 2.4 23.6 1.0
O A:HOH2105 2.4 28.2 1.0
O A:HOH2102 2.4 33.1 1.0
O A:HOH2103 2.5 29.9 1.0
OD1 A:ASP101 2.6 18.5 1.0
CG A:ASP101 2.8 17.4 1.0
O A:HOH2106 3.5 40.1 1.0
CB A:ASP101 4.3 15.3 1.0
O A:ASP101 4.4 16.1 1.0

Holmium binding site 3 out of 3 in 2bpu

Go back to Holmium Binding Sites List in 2bpu
Holmium binding site 3 out of 3 in the The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 3 of The Kedge Holmium Derivative of Hen Egg-White Lysozyme at High Resolution From Single Wavelength Anomalous Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ho1136

b:19.9
occ:1.00
 O A:HOH2109 1.8 8.4 1.0
O A:HOH2108 2.0 13.0 1.0
O A:HOH2111 2.1 33.2 1.0
OD2 A:ASP52 2.2 14.0 1.0
O A:HOH2110 2.3 21.4 1.0
O A:HOH2107 2.4 14.2 1.0
O A:HOH2030 3.5 33.0 1.0
CG A:ASP52 3.5 11.5 1.0
OD1 A:ASN46 4.1 15.1 1.0
O A:HOH2051 4.3 29.3 1.0
OD1 A:ASP52 4.3 10.2 1.0
OE1 A:GLU35 4.4 12.0 1.0
O A:HOH2033 4.4 20.8 1.0
CB A:ASP52 4.4 10.0 1.0
O A:HOH2032 4.5 20.0 1.0
O A:HOH2031 4.6 16.3 1.0
NE2 A:GLN57 4.8 7.8 1.0
CB A:GLN57 4.9 9.1 1.0

Reference:

J.Jakoncic, M.Di Michiel, Z.Zhong, V.Honkimaki, Y.Jouanneau, V.Stojanoff. Anomalous Diffraction at Ultra-High Energy For Protein Crystallography. J.Appl.Crystallogr. V. 39 831 2006.
ISSN: ISSN 0021-8898
DOI: 10.1107/S0021889806036387
Page generated: Fri Aug 8 11:37:52 2025

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